Sensitivity analysis is important for determining the parameters in the model calibration process.In our study,a variance-based global sensitivity analysis(extended Fourier amplitude sensitivity test,EFAST)was applied...Sensitivity analysis is important for determining the parameters in the model calibration process.In our study,a variance-based global sensitivity analysis(extended Fourier amplitude sensitivity test,EFAST)was applied to an agro-hydrological model(the SWAP(Soil-Water-Atmosphere-Plant model)model).The sensitivities of 20 parameters belonging to 4 categories(soil hydraulics,solute transport,root water uptake,and environmental stresses)for the simulated accumulated transpiration,dry matter(DM),and yield of sunflowers were analyzed under three nitrogen application rates(N1,N2,and N3),four salinity levels(S1,S2,S3,and S4),and three root distributions(R1,R2,and R3).The results indicated that for predominantly loamy soils,the high-impact parameters for accumulated transpiration,DM,and yield were the soil hydraulic parameters(αand n),critical stress index for compensatory root water uptake(ωc),the salt level at which salt stress starts(Pi),the decline of root water uptake above Pi(SSF),residual water content(θr),saturated water content(θs),and relative uptake of solutes by roots(TSCF).We also found that nitrogen application did not change the order of the parameter impacts on accumulated transpiration,DM,and yield.However,TSCF replacedαas the highest-impact parameter for the accumulated transpiration,DM,and yield at high salinity levels(S2 and S3).Furthermore,αwas also the highest-impact parameter for DM and yield under different root distributions,but the highest-impact parameters for transpiration wereωc,α,andθs under R1,R2,and R3,respectively.Nitrogen application could be neglected when considering the interactive effects of nitrogen application,salinity level,and root distribution on the transpiration,DM,and yield.Additionally,the mean values and uncertainties of the transpiration,DM,and yield were similar in all scenarios,except S3,which showed a sharp decrease in the mean values.We suggest determining the above eight parameters(α,n,ωc,Pi,SSF,θr,θs,and TSCF)and the saturated vertical hydraulic conductivity(Ks)based on rigorous calibrations with direct or indirect local measurements using economical methods(e.g.,a literature review),with limited observations for other parameters when using the SWAP model and other similar agro-hydrological models.展开更多
Chemically defined medium is widely used for culturing mouse embryonic stem cells(mESCs),in which N2B27 works as a substitution for serum,and GSK3βand MEK inhibitors(2i)help to promote ground-state pluripo-tency.Howe...Chemically defined medium is widely used for culturing mouse embryonic stem cells(mESCs),in which N2B27 works as a substitution for serum,and GSK3βand MEK inhibitors(2i)help to promote ground-state pluripo-tency.However,recent studies suggested that MEKi might cause irreversible defects that compromise the developmental potential of mESCs.Here,we demon-strated the deficient bone morphogenetic protein(BMP)signal in the chemically defined condition is one of the main causes for the impaired pluripotency.Mechanisti-cally,activating the BMP signal pathway by BMP4 could safeguard the chromosomal integrity and proliferation capacity of mESCs through regulating downstream tar-gets Ube2s and Chmp4b.More importantly,BMP4 pro-motes a distinct in vivo developmental potential and a long-term pluripotency preservation.Besides,the pluripotent improvements driven by BMP4 are superior to those by attenuating MEK suppression.Taken together,our study shows appropriate activation of BMP signal is essential for regulating functional pluripotency and reveals that BMP4 should be applied in the serum-free culture system.展开更多
Embryonic stem (ES) cells derived from the pre-implantation blastocyst-stage embryos have been widely used to investigate the molecular events determining pluripotency and cell lineage differentiation. As the first ...Embryonic stem (ES) cells derived from the pre-implantation blastocyst-stage embryos have been widely used to investigate the molecular events determining pluripotency and cell lineage differentiation. As the first discovered ES-specific transcription factor, Oct4 has been considered as the core pluripotency factor of ES cells. In the present study, we successfully established seven ES lines from the blastocysts collected from female OG2 (Oct4-GFP transgenic) mice, which have been crossed with male rtTA transgenic mice. The pluripotency of the ES cell lines can be visualized by the expression of Oct4-GFP under fluorescent microscopy and germ-line transmission capability has been further confirmed. More importantly, the presence of rtTA could induce transgene's expression with the help of doxycycline. Therefore, these ES cell lines provide an excellent tool to further discover novel factors affecting pluripotency and to investigate the molecular mechanism of reprogramming in defined transcription factors mediated nuclear reprogramming.展开更多
Extensive studies have been performed to describe the phenotypic changes occurring during malignant transformation of the prostate.However,the cell types and associated changes that contribute to the development of pr...Extensive studies have been performed to describe the phenotypic changes occurring during malignant transformation of the prostate.However,the cell types and associated changes that contribute to the development of prostate diseases and cancer remain elusive,largely due to the heterogeneous composition of prostatic tissues.Here,we conduct a comprehensive evaluation of four human prostate tissues by singlecell RNA sequencing(sc RNA-seq)to analyze their cellular compositions.We identify 18 clusters of cell types,each with distinct gene expression profiles and unique features;of these,one cluster of epithelial cells(Ep)is found to be associated with immune function.In addition,we characterize a special cluster of fibroblasts and aberrant signaling changes associated with prostate cancer(PCa).Moreover,we provide insights into the epithelial changes that occur during the cellular senescence and aging.These results expand our understanding of the unique functional associations between the diverse prostatic cell types and the contributions of specific cell clusters to the malignant transformation of prostate tissues and PCa development.展开更多
Suitable reference genes are one of the necessary conditions for obtaining reliable results by real-time fluorescence quantitative PCR(qPCR).In this study,the expression of the 10 common candidate reference genes(18s ...Suitable reference genes are one of the necessary conditions for obtaining reliable results by real-time fluorescence quantitative PCR(qPCR).In this study,the expression of the 10 common candidate reference genes(18s rRNA,rps27,cnbp,rpl7,ube2,hsp-at,gapdh,β-actin,rpl13a,1-ef1a)at different developmental stages of gonad and embryo of Takifugu bimaculatus were analyzed by qPCR.And the expression stability of these reference genes is analyzed by GeNorm,NormFinder and Bestkeeper softwares.The results showed that the expression stability of 1-ef1a was the highest(p<0.05)combined with the results of three analysis softwares,and the optimal number of reference genes was 3,which were 1-ef1a,hsp-at and rps27.Based on this result,we analyzed the expression of objective genes(foxl2 and dmrt1)at different developmental stages(early,medium-term and late)of gonads and embryos(eye vesicle stage,motility stage,heart anlage stage,retinal pigmentation stage,newly hatched larva)of T.bimaculatus by qPCR.Among which the highest expression level of foxl2 was in the middle stage of ovary(p<0.05),and dmrt1 was expressed in the early stage of testis with the highest level(p<0.05).The expression levels of foxl2 and dmrt1 in the early stages of embryonic development were low or even almost non-existent,and had a slight increase in the late embryonic development(newly hatched larva).The expression profile of objective genes are consistent with their roles in the development of gonads and embryos,which indicates that 1-ef1a,hsp-at and rps27 are the suitable reference gene combination for detecting the expression of objective genes by qPCR in gonads and embryos of T.bimaculatus.This research also provides the reliability data for screening the reference genes by qPCR in fish.展开更多
基金This work was supported by the Key Project of Zhejiang Provincial Natural Science Foundation(Grant No.LZ22E050001)the National Natural Science Foundation of China(Grant No.82001918).
基金the financial support from the Major Program of the National Natural Science Foundation of China(Nos.51879196 and 51790533)the China Postdoctoral Science Foundation Funded Project(No.2020M682475)the Fundamental Research Funds for the Central Universities,China(No.IWHR-SKL-KF201814)。
文摘Sensitivity analysis is important for determining the parameters in the model calibration process.In our study,a variance-based global sensitivity analysis(extended Fourier amplitude sensitivity test,EFAST)was applied to an agro-hydrological model(the SWAP(Soil-Water-Atmosphere-Plant model)model).The sensitivities of 20 parameters belonging to 4 categories(soil hydraulics,solute transport,root water uptake,and environmental stresses)for the simulated accumulated transpiration,dry matter(DM),and yield of sunflowers were analyzed under three nitrogen application rates(N1,N2,and N3),four salinity levels(S1,S2,S3,and S4),and three root distributions(R1,R2,and R3).The results indicated that for predominantly loamy soils,the high-impact parameters for accumulated transpiration,DM,and yield were the soil hydraulic parameters(αand n),critical stress index for compensatory root water uptake(ωc),the salt level at which salt stress starts(Pi),the decline of root water uptake above Pi(SSF),residual water content(θr),saturated water content(θs),and relative uptake of solutes by roots(TSCF).We also found that nitrogen application did not change the order of the parameter impacts on accumulated transpiration,DM,and yield.However,TSCF replacedαas the highest-impact parameter for the accumulated transpiration,DM,and yield at high salinity levels(S2 and S3).Furthermore,αwas also the highest-impact parameter for DM and yield under different root distributions,but the highest-impact parameters for transpiration wereωc,α,andθs under R1,R2,and R3,respectively.Nitrogen application could be neglected when considering the interactive effects of nitrogen application,salinity level,and root distribution on the transpiration,DM,and yield.Additionally,the mean values and uncertainties of the transpiration,DM,and yield were similar in all scenarios,except S3,which showed a sharp decrease in the mean values.We suggest determining the above eight parameters(α,n,ωc,Pi,SSF,θr,θs,and TSCF)and the saturated vertical hydraulic conductivity(Ks)based on rigorous calibrations with direct or indirect local measurements using economical methods(e.g.,a literature review),with limited observations for other parameters when using the SWAP model and other similar agro-hydrological models.
基金This work was supported by the National Key R&D Program of China(2020YFA0112500 and 2021YFA1100300)the National Natural Science Foundation of China(31721003,31820103009,92168205,32070857 and 31871446)+3 种基金the Young Elite Scientist Sponsorship Program by CAST(2018QNRC001)the key project of the Science and Technology of Shanghai Municipality(19JC1415300)the Shanghai Rising-Star Program(19QA1409600)the Shanghai municipal medical and health discipline construction projects(no.2017ZZ02015).
文摘Chemically defined medium is widely used for culturing mouse embryonic stem cells(mESCs),in which N2B27 works as a substitution for serum,and GSK3βand MEK inhibitors(2i)help to promote ground-state pluripo-tency.However,recent studies suggested that MEKi might cause irreversible defects that compromise the developmental potential of mESCs.Here,we demon-strated the deficient bone morphogenetic protein(BMP)signal in the chemically defined condition is one of the main causes for the impaired pluripotency.Mechanisti-cally,activating the BMP signal pathway by BMP4 could safeguard the chromosomal integrity and proliferation capacity of mESCs through regulating downstream tar-gets Ube2s and Chmp4b.More importantly,BMP4 pro-motes a distinct in vivo developmental potential and a long-term pluripotency preservation.Besides,the pluripotent improvements driven by BMP4 are superior to those by attenuating MEK suppression.Taken together,our study shows appropriate activation of BMP signal is essential for regulating functional pluripotency and reveals that BMP4 should be applied in the serum-free culture system.
基金supported by the Ministry of Science and Technology of China(Nos.2010CB944900 and 2011CB964800)
文摘Embryonic stem (ES) cells derived from the pre-implantation blastocyst-stage embryos have been widely used to investigate the molecular events determining pluripotency and cell lineage differentiation. As the first discovered ES-specific transcription factor, Oct4 has been considered as the core pluripotency factor of ES cells. In the present study, we successfully established seven ES lines from the blastocysts collected from female OG2 (Oct4-GFP transgenic) mice, which have been crossed with male rtTA transgenic mice. The pluripotency of the ES cell lines can be visualized by the expression of Oct4-GFP under fluorescent microscopy and germ-line transmission capability has been further confirmed. More importantly, the presence of rtTA could induce transgene's expression with the help of doxycycline. Therefore, these ES cell lines provide an excellent tool to further discover novel factors affecting pluripotency and to investigate the molecular mechanism of reprogramming in defined transcription factors mediated nuclear reprogramming.
基金funded by the Youth Science Foundation of Guangxi Medical University(GXMUYSF201810)the National Natural Science Foundation of China(81901538,81670750,81770759)+3 种基金the Sigrid Juse’lius Foundation and the Recruitment Fund of Fudan Universitythe National Key Research and Development Program of China(2017YFC0908000)the Major Project of Guangxi Innovation Driven(AA18118016)the Guangxi Key Laboratory for Genomic and Personalized Medicine(16-380-54,17-259-45,19-050-22,19-185-33,and 20-065-33)。
文摘Extensive studies have been performed to describe the phenotypic changes occurring during malignant transformation of the prostate.However,the cell types and associated changes that contribute to the development of prostate diseases and cancer remain elusive,largely due to the heterogeneous composition of prostatic tissues.Here,we conduct a comprehensive evaluation of four human prostate tissues by singlecell RNA sequencing(sc RNA-seq)to analyze their cellular compositions.We identify 18 clusters of cell types,each with distinct gene expression profiles and unique features;of these,one cluster of epithelial cells(Ep)is found to be associated with immune function.In addition,we characterize a special cluster of fibroblasts and aberrant signaling changes associated with prostate cancer(PCa).Moreover,we provide insights into the epithelial changes that occur during the cellular senescence and aging.These results expand our understanding of the unique functional associations between the diverse prostatic cell types and the contributions of specific cell clusters to the malignant transformation of prostate tissues and PCa development.
基金This work was supported by Natural Science Foundation of Fujian Province(2018J01451)Regional Demonstration of Marine Economy Innovative Development Project(16PZY002SF18)+3 种基金Fujian Engineering Research Center of Aquatic Breeding and Healthy Aquaculture(DF201905)Ornamental Aquarium Engineering Research Center in University of Fujian ProvinceUndergraduate Innovation Project of Fujian Province(201810390064,201910390047)College Students innovation and entrepreneurship training program of Jimei University(2020xj053,2020xj059)。
文摘Suitable reference genes are one of the necessary conditions for obtaining reliable results by real-time fluorescence quantitative PCR(qPCR).In this study,the expression of the 10 common candidate reference genes(18s rRNA,rps27,cnbp,rpl7,ube2,hsp-at,gapdh,β-actin,rpl13a,1-ef1a)at different developmental stages of gonad and embryo of Takifugu bimaculatus were analyzed by qPCR.And the expression stability of these reference genes is analyzed by GeNorm,NormFinder and Bestkeeper softwares.The results showed that the expression stability of 1-ef1a was the highest(p<0.05)combined with the results of three analysis softwares,and the optimal number of reference genes was 3,which were 1-ef1a,hsp-at and rps27.Based on this result,we analyzed the expression of objective genes(foxl2 and dmrt1)at different developmental stages(early,medium-term and late)of gonads and embryos(eye vesicle stage,motility stage,heart anlage stage,retinal pigmentation stage,newly hatched larva)of T.bimaculatus by qPCR.Among which the highest expression level of foxl2 was in the middle stage of ovary(p<0.05),and dmrt1 was expressed in the early stage of testis with the highest level(p<0.05).The expression levels of foxl2 and dmrt1 in the early stages of embryonic development were low or even almost non-existent,and had a slight increase in the late embryonic development(newly hatched larva).The expression profile of objective genes are consistent with their roles in the development of gonads and embryos,which indicates that 1-ef1a,hsp-at and rps27 are the suitable reference gene combination for detecting the expression of objective genes by qPCR in gonads and embryos of T.bimaculatus.This research also provides the reliability data for screening the reference genes by qPCR in fish.